Working on downloaded deepvariant sif file in the miniwdl workflow

[priyambial123]

I am working with miniwdl workflow and I could not download the deepvariant docker image in the Ubuntu cluster. So I downloaded the image and converted to sif image in the local system and transferred into the miniwdl_singularity_cache folder (in Ubuntu cluster). When I run the workflow, still it tries to download the docker image ,build it and fails. Is there a way to over ride these downloading steps and use the deepvariant.sif file in the miniwdl_singularity_cache folder. Please find the attached snapshot of the folder with docker images

Thank you

[williamrowell]

The current release of the workflow, v1.1.1, does not use DeepVariant v1.6. It should be using v1.5. To make sure you're using the current supported release, clone the workflow code like:

git clone \
  --depth 1 --branch v1.1.1 \
  --recursive \
  https://github.com/PacificBiosciences/HiFi-human-WGS-WDL.git

--branch v1.1.1 ensures that you're pulling the supported release branch. --recursive ensures that you're pulling the matched version of the wdl-common submodule

Once you've cloned the supported version of the workflow, if you're still having problems with miniwdl pulling the DeepVariant image, you can pull the image manually and rename it in your cache folder like:

singularity pull docker://gcr.io/deepvariant-docker/deepvariant:1.5.0

# miniwdl expects a very specific file name format in this cache
mv deepvariant_1.5.0.sif docker___gcr.io_deepvariant-docker_deepvariant_1.5.0.sif